Project ID: plumID:22.017
Source: FES/plumed.dat
Originally used with PLUMED version: 2.8
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
Click on the labels of the actions for more information on what each action computes
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# --- (1) ATOMS DEFINITIONS and ALIGNMENT ---
protein:GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=1-3232the numerical indexes for the set of atoms in the groupWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=proteinthe atoms that make up a molecule that you wish to alignFIT_TO_TEMPLATEThis action is used to align a molecule to a template. More detailsSTRIDE=1the frequency with which molecules are reassembledREFERENCE=fit_tem.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMALthe manner in which RMSD alignment is performed
WO:GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=3251-47362:3 # water moleculesthe numerical indexes for the set of atoms in the group
G:GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=3236 #ligand selected atom H:the numerical indexes for the set of atoms in the groupGROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=2480 #Bindong pose selected atomthe numerical indexes for the set of atoms in the group
lig:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=3233,3236,3237,3240,3241,3243,3245,3247,3249 #Carbon and Nitrogen atoms of the ligandthe group of atoms that you are calculating the Gyration Tensor for
# Hydration spots v1:FIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=3.710,3.472,4.707 v2:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=3.600,3.300,4.400 v3:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=3.731,3.025,3.992 v4:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=3.705,3.084,3.683 v5:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=3.883,3.174,3.461 v6:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=4.040,3.264,3.306 v7:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=4.239,3.319,3.236 v8:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=4.485,3.286,3.225 v9:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=4.701,3.182,3.332 v10:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=4.466,3.382,3.446 v11:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=4.461,3.424,3.659 v12:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=4.495,3.335,3.920 v13:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=4.295,3.430,3.876 v14:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=4.070,3.450,3.834 v15:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=3.887,3.241,3.875 v16:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=3.815,3.292,4.144coordinates of the virtual atom
# --- (2) DESCRIPTORS --- NG:COORDINATIONCalculate coordination numbers. More detailsGROUPA=GFirst list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=0.6}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.0The cutoff for the neighbor listNL_STRIDE=20 NH:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=HFirst list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.35 NN=6 MM=10 D_MAX=0.8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.0The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor list
cvwo1:COORDINATIONCalculate coordination numbers. More detailsGROUPA=v1First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.0The cutoff for the neighbor listNL_STRIDE=20 cvwo2:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v2First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.0The cutoff for the neighbor listNL_STRIDE=20 cvwo3:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v3First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.0The cutoff for the neighbor listNL_STRIDE=20 cvwo4:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v4First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.0The cutoff for the neighbor listNL_STRIDE=20 cvwo5:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v5First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.0The cutoff for the neighbor listNL_STRIDE=20 cvwo6:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v6First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.0The cutoff for the neighbor listNL_STRIDE=20 cvwo7:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v7First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.0The cutoff for the neighbor listNL_STRIDE=20 cvwo8:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v8First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.0The cutoff for the neighbor listNL_STRIDE=20 cvwo9:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v9First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.0The cutoff for the neighbor listNL_STRIDE=20 cvwo10:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v10First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.0The cutoff for the neighbor listNL_STRIDE=20 cvwo11:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v11First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.0The cutoff for the neighbor listNL_STRIDE=20 cvwo12:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v12First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.0The cutoff for the neighbor listNL_STRIDE=20 cvwo13:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v13First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.0The cutoff for the neighbor listNL_STRIDE=20 cvwo14:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v14First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.0The cutoff for the neighbor listNL_STRIDE=20 cvwo15:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v15First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.0The cutoff for the neighbor listNL_STRIDE=20 cvwo16:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v16First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=2.0The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor list
vwo1:MATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo1the input to this functionFUNC=(x/1.5)-1.0the function you wish to evaluatePERIODIC=NO #normalized descriptors vwo2:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo2the input to this functionFUNC=(x/1.5)-1.0the function you wish to evaluatePERIODIC=NO vwo3:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo3the input to this functionFUNC=(x/1.5)-1.0the function you wish to evaluatePERIODIC=NO vwo4:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo4the input to this functionFUNC=(x/1.5)-1.0the function you wish to evaluatePERIODIC=NO vwo5:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo5the input to this functionFUNC=(x/1.5)-1.0the function you wish to evaluatePERIODIC=NO vwo6:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo6the input to this functionFUNC=(x/1.5)-1.0the function you wish to evaluatePERIODIC=NO vwo7:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo7the input to this functionFUNC=(x/1.5)-1.0the function you wish to evaluatePERIODIC=NO vwo8:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo8the input to this functionFUNC=(x/1.5)-1.0the function you wish to evaluatePERIODIC=NO vwo9:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo9the input to this functionFUNC=(x/1.5)-1.0the function you wish to evaluatePERIODIC=NO vwo10:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo10the input to this functionFUNC=(x/1.5)-1.0the function you wish to evaluatePERIODIC=NO vwo11:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo11the input to this functionFUNC=(x/1.5)-1.0the function you wish to evaluatePERIODIC=NO vwo12:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo12the input to this functionFUNC=(x/1.5)-1.0the function you wish to evaluatePERIODIC=NO vwo13:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo13the input to this functionFUNC=(x/1.5)-1.0the function you wish to evaluatePERIODIC=NO vwo14:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo14the input to this functionFUNC=(x/1.5)-1.0the function you wish to evaluatePERIODIC=NO vwo15:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo15the input to this functionFUNC=(x/1.5)-1.0the function you wish to evaluatePERIODIC=NO vwo16:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo16the input to this functionFUNC=(x/1.5)-1.0the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
FG:MATHEVALAn alias to the ef CUSTOM function. More detailsARG=NGthe input to this functionFUNC=(x/1.5)-1.0the function you wish to evaluatePERIODIC=NO FH:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=NHthe input to this functionFUNC=(x/2.5)-1.0the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
# ---(3) Funnel --- cyl:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=v14,ligthe pair of atom that we are calculating the distance betweenCOMPONENTSradius:calculate the x, y and z components of the distance separately and store them as labelMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cyl.x,cyl.ythe input to this functionVAR=x,ythe names to give each of the arguments in the functionFUNC=sqrt(x*x+y*ythe function you wish to evaluatePERIODIC=NO funnel:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=radius,cyl.zthe input to this functionVAR=r,zthe names to give each of the arguments in the functionFUNC=(r+0.5*(-1.6+z))*step(-z+1.2)+(r-0.2)*step(z-1.2the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsAT=0the positions of the wallARG=funnelthe arguments on which the bias is actingKAPPA=10000.0the force constant for the wallLABEL=funnelwalla label for the action so that its output can be referenced in the input to other actions
# ---(4) Wall on distance to prevent exit of ligandLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsAT=0.2the positions of the wallARG=cyl.zthe arguments on which the bias is actingKAPPA=5000.0the force constant for the wallEXP=2the powers for the wallsLABEL=lower_wall_za label for the action so that its output can be referenced in the input to other actionsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsAT=2.5the positions of the wallARG=cyl.zthe arguments on which the bias is actingKAPPA=5000.0the force constant for the wallEXP=2the powers for the wallsLABEL=upper_wall_za label for the action so that its output can be referenced in the input to other actions
# ---(5) This rmsd restricts the CA momevement of the entire protein rmsdINIT:RMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=fit_tem.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMALthe manner in which RMSD alignment is performedUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=rmsdINITthe arguments on which the bias is actingAT=0.09the positions of the wallKAPPA=420000the force constant for the wallEXP=2the powers for the wallsOFFSET=0the offset for the start of the wallLABEL=rmsdwallINITa label for the action so that its output can be referenced in the input to other actions
# --- (6) DEEP-LDA CV --- s:PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More detailsFILE=CV_16V_G_H_1.ptFilename of the PyTorch compiled modelARG=vwo14,vwo3,vwo5,vwo9,vwo7,vwo10,vwo12,vwo11,vwo6,vwo2,vwo16,vwo1,vwo15,vwo8,vwo13,vwo4,FG,FH sw:the input for this action is the scalar output from one or more other actionsMATHEVALAn alias to the ef CUSTOM function. More detailsARG=s.node-0the input to this functionFUNC=x+x^3the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsAT=3.0the positions of the wallARG=swthe arguments on which the bias is actingKAPPA=4000.0the force constant for the wallEXP=2the powers for the wallsLABEL=upper_swa label for the action so that its output can be referenced in the input to other actionsLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsAT=-3.0the positions of the wallARG=swthe arguments on which the bias is actingKAPPA=5000.0the force constant for the wallEXP=2the powers for the wallsLABEL=lower_swa label for the action so that its output can be referenced in the input to other actions
# --- (7) DEEP-TICA CV ---
t:PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More detailsFILE=deeptica_all_lag_0.07model_all.ptFilename of the PyTorch compiled modelARG=vwo14,vwo3,vwo5,vwo9,vwo7,vwo10,vwo12,vwo11,vwo6,vwo2,vwo16,vwo1,vwo15,vwo8,vwo13,vwo4,FG,FH st:the input for this action is the scalar output from one or more other actionsMATHEVALAn alias to the ef CUSTOM function. More detailsARG=t.node-0the input to this functionFUNC=1*xthe function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
# --- (8) OPES ---OPES_METAD...On-the-fly probability enhanced sampling with metadynamics-like target distribution. More detailsLABEL=opesa label for the action so that its output can be referenced in the input to other actionsARG=cyl.z,swthe input for this action is the scalar output from one or more other actionsFILE=../Kernels.dataa file in which the list of all deposited kernels is storedSTATE_RFILE=../compressed.Kernelsread from this file the compressed kernels and all the info needed to RESTART the simulationSTATE_WFILE=../compressed.Kernelswrite to this file the compressed kernels and all the info needed to RESTART the simulationPACE=500the frequency for kernel depositionBARRIER=50the free energy barrier to be overcomeRESTART=NOallows per-action setting of restart (YES/NO/AUTO)STATE_WSTRIDE=5000number of MD steps between writing the STATE_WFILEWALKERS_MPI... OPES_METADswitch on MPI version of multiple walkersPrint quantities to a file. More detailsARGthe input for this action is the scalar output from one or more other actionsSTRIDE=250the frequency with which the quantities of interest should be outputFILE=COLVAR_allthe name of the file on which to output these quantitiesFMT=%8.4fthe format that should be used to output real numbers